Mercurial > repos > thanhlv > snippy
diff snippy.xml @ 8:922cfa35669c draft
planemo upload commit bacf06ead51adad153dd083d60a4e6643637b978
| author | thanhlv |
|---|---|
| date | Tue, 24 Sep 2019 09:56:49 -0400 |
| parents | cfe622189417 |
| children |
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--- a/snippy.xml Mon Sep 23 18:38:18 2019 -0400 +++ b/snippy.xml Tue Sep 24 09:56:49 2019 -0400 @@ -42,6 +42,8 @@ --se '$fastq_input.fastq_input_single' #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" --peil '$fastq_input.fastq_input_interleaved' + #elif str( $fastq_input.fastq_input_selector ) == "contigs" + --ctgs '$fastq_input.fastq_input_contigs' #end if && @@ -55,6 +57,8 @@ #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "contigs" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_contigs.element_identifier) #end if mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && @@ -90,6 +94,7 @@ <option value="single">Single</option> <option value="paired_collection">Paired Collection</option> <option value="paired_iv">Paired Interleaved</option> + <option value="contigs">Assemblies</option> </param> <when value="paired"> <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> @@ -104,6 +109,9 @@ <when value="paired_iv"> <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> </when> + <when value="contigs"> + <param name="fastq_input_contigs" type="data" format="fasta,fasta.gz" label="Select fasta file"/> + </when> </conditional> <section name="adv" title="Advanced parameters" expanded="false">